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Only apply the patch forward, and ensure the working directory is correct.
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Makefile.pre.in

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@@ -935,7 +935,7 @@ $(BUILDPYTHON)-gdb.py: $(SRC_GDB_HOOKS)
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# known modifications to the source tree before building.
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.PHONY: app-store-compliance
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app-store-compliance:
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patch -p1 @APP_STORE_COMPLIANCE_PATCH_FLAGS@ < $(srcdir)/$(APP_STORE_COMPLIANCE_PATCH)
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patch @APP_STORE_COMPLIANCE_PATCH_FLAGS@ --forward --strip=1 --directory="$(srcdir)" --input "$(APP_STORE_COMPLIANCE_PATCH)"
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# This rule is here for OPENSTEP/Rhapsody/MacOSX. It builds a temporary
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# minimal framework (not including the Lib directory and such) in the current

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